[gmx-users] Structure optimization failure

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 15:09:10 CEST 2012

On 6/29/12 9:04 AM, massimo sandal wrote:
> On 29 Jun 2012 14:08, "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  >
>  > The settings in my tutorial are for use with OPLS-AA and are thus not
> suitable for a simulation with CHARMM.  Cutoffs and other aspects will be different.
> This is interesting. In general, where can you find optimal mdp settings for
> each force field?

By reading the primary literature for how each force field was derived.  The 
parameters are only guaranteed to work within the context of correct cutoffs, 
electrostatic schemes, neighborlist update interval, water model used, etc. 
Some older force fields have been demonstrated to work well with PME even if 
originally derived with RF or some other method, but generally the other 
settings must adhere to the original parameterization.  Some force fields can be 
very sensitive to these incorrect settings.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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